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- PDB-3fjw: Crystal Structure Analysis of Fungal Versatile Peroxidase from Pl... -

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Basic information

Entry
Database: PDB / ID: 3fjw
TitleCrystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii
ComponentsVersatile peroxidase VPL2
KeywordsOXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / protoporphyrin IX / glycoprotein ELECTRON TRANSFER / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / MN-INDEPENDENT OXIDATION PHENOLIC NON-PHENOLIC AROMATICS / MNII OXIDATION / PEROXIDASE / POLYVALENT PEROXIDASE / Heme / glycoprotein / Hydrogen peroxide / Iron / Manganese / Metal-binding / Secreted / Zymogen
Function / homology
Function and homology information


versatile peroxidase / reactive-black-5:hydrogen-peroxide oxidoreductase activity / manganese peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site ...Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / alpha-D-mannopyranose / : / Versatile peroxidase VPL2
Similarity search - Component
Biological speciesPleurotus eryngii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPiontek, K. / Martinez, A.T. / Choinowski, T. / Plattner, D.A.
CitationJournal: To be Published
Title: Structural and Site-directed Mutagenesis Study of Versatile Peroxidase Oxidizing both Mn(II) and Aromatic Substrates
Authors: Piontek, K. / Choinowski, T. / Perez-Boada, M. / Ruiz-Duenas, F.J. / Martinez, M.J. / Plattner, D.A. / Martinez, A.T.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Versatile peroxidase VPL2
B: Versatile peroxidase VPL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,92320
Polymers69,2112
Non-polymers3,71118
Water8,143452
1
A: Versatile peroxidase VPL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,46110
Polymers34,6061
Non-polymers1,8569
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Versatile peroxidase VPL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,46110
Polymers34,6061
Non-polymers1,8569
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.141, 92.762, 113.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Versatile peroxidase VPL2 / Versatile liquid phase peroxidase 2


Mass: 34605.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pleurotus eryngii (fungus) / Strain: IJFM A169 / References: UniProt: O94753, versatile peroxidase

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Sugars , 3 types, 10 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 460 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8.0mg/ml protein in 10mM Na-citrate pH 4.0, 1.9M ammonium sulphate, 6% PEG 400, 100mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8499 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8499 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 20657 / Num. obs: 19316 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.112 / Net I/σ(I): 11.3

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QPA

1qpa


Resolution: 2.8→39.17 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.863 / SU B: 5.741 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24629 942 5.1 %RANDOM
Rwork0.15832 ---
obs0.16277 17415 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.013 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2--0.66 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 230 452 5548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225266
X-RAY DIFFRACTIONr_angle_refined_deg0.7472.0467210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0925.385208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34615714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6721518
X-RAY DIFFRACTIONr_chiral_restr0.0490.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024012
X-RAY DIFFRACTIONr_nbd_refined0.2340.32795
X-RAY DIFFRACTIONr_nbtor_refined0.3260.53730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.5588
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2770.512
X-RAY DIFFRACTIONr_mcbond_it0.67523358
X-RAY DIFFRACTIONr_mcangle_it1.18635338
X-RAY DIFFRACTIONr_scbond_it0.64222047
X-RAY DIFFRACTIONr_scangle_it1.01631868
LS refinement shellResolution: 2.8→2.993 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.335 159 -
Rwork0.142 3150 -
obs--95.2 %

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